Description

This is a major bug fix release - all model-free users of relax version 1.3.6 must upgrade to this version. The fatal bug is that the prolate diffusion tensor when initialised with D_a set to zero will be converted to an oblate tensor. Other bugs fixed include support for volume integration together with replicated spectra, the scipy dependency now bing optional, 32-bit GNU/Linux test suite fixes, and better support for the reading of old version 1.2.x results files. An additional feature is that the relax packages/modules can now be imported and used outside of relax.

Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).

CHANGES file

Version 1.3.7
(10 January 2011, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.7

Features

Shifted the relax installation path variable from __main__ into the status singleton object, allowing relax modules to be imported outside of relax.
Shifted the global relax debug flag from __main__.debug to the relax status singleton, allowing the flag to be defined even when imported from outside of relax.

Changes

Speed up of the relaxation curve-fitting system tests.
The sample_scripts/full_analysis.py script has been renamed to sample_scripts/dauvergne_protocol.py[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b].
Improvements to the test suite final print out with a table of skipped tests.
The data pipe system test is avoiding the frame order data pipe, allowing the test to pass without scipy installed.
The alignment tensor system test now uses the N-state model rather than frame order so it is always tested.
The frame order system and unit tests are skipped if scipy is not installed.
The frame order analysis is disabled if scipy is not installed.
The data pipe generic code now uses dep_check to see if the relaxation curve-fitting is available.
The system tests now use the RelaxTestLoader to allow tests to be skipped.
The unit vector system tests using scientific python are now being skipped if the package is not installed.
The structure system tests involving scientific python are now skipped if the package is not installed.
The RelaxTestLoader has been added as a replacement for unittest.TestLoader to handle the skipping of tests when optional Python packages are not installed.
Shifted the status singleton instantiation to the import level in all modules, saving execution time.
Big code cleanups in unit_test_runner.py.

Bugfixes

Peak intensity errors can now be calculated when using volume integration and replicated spectra (bug #17457).
Failure of the prolate diffusion tensor in model-free analysis - if the tensor is initialised with Da = 0, the tensor is converted to being oblate. This was introduced in relax version 1.3.6.
relax can now operate without scipy being installed.
Updated four model-free optimisation system tests to pass under 32-bit Linux.
Made the N_state_model.test_pcs_fit_zero_pos system test less stringent so it passes on 32-bit Linux.
The model_free _model_setup() method should handle no model-free model being set when reading relax 1.2 results files (bug #17417).

Announcements

If you would like to receive announcements about new relax versions, please subscribe to the relax announcement mailing list. This list only receives ~10 emails per year. It is archived at the SourceForge archives and in The Mail Archive.

References

[*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and Gooley, P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. Mol. BioSyst., 3(7), 483–494. (DOI: [http://dx.doi.org/10.1039/b702202f 10.1039/b702202f).
[*d'Auvergne and Gooley, 2008b] d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133. (DOI: 10.1007/s10858-007-9213-3).

relax 1.3.7